It is a job that is on the list to sort out but not at this time of year. I budget each year to improve my car and next month I am having a stainless steel exhaust fitted.
My ideal solution to the roof is to have it completely recovered and this would be done through the winter. To start with I would probably remove the windscreen trims to see what that reveals.
As you can appreciate it is not a straight forward job as you probably have to disturb the targa seal and the possibility of removing the windscreen. Did you have to remove the windscreen on yours to sort out the rust?